[gmx-users] New residue in FF does not bond to others.

[Justin Lemkul]

The problem is in atom naming.  You have used MN1 and MC3 for the equivalent of 
amino acid N and C atoms, respectively.  pdb2gmx chokes here, because Phe-65 
tries to make a bond to the +N atom, which it does not find until it runs into 
Ser-69.  Likewise with the C atom in CH6.  If you rename these atoms (MN1->N, 
MC3->C) in the .rtp and .hdb, everything works fine.

If there are still missing parameters for interactions, you'll have to figure 
that out.  There are several missing inter-residue angles and dihedrals in your 
.rtp entry for CH6.

-Justin

On 8/7/14, 11:48 AM, Dawid das wrote:
> http://www.speedyshare.com/9EhEf/charm27-files.tar.bz2
> http://www.speedyshare.com/AMWM7/mCherry7.tar.bz2
>
> Like I said they are the same except two extra lines in aminoacids.rtp file.
>
>
> 2014-08-07 2:27 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
>
>>
>>
>> On 8/6/14, 1:36 PM, Dawid das wrote:
>>
>>> These are lines that cause trouble:
>>>
>>> ERROR 1 [file mCherry7.top, line 18183]:
>>>     No default U-B types
>>>
>>>
>>> ERROR 2 [file mCherry7.top, line 18250]:
>>>     No default U-B types
>>>
>>>
>>> ERROR 3 [file mCherry7.top, line 25379]:
>>>     No default Proper Dih. types
>>>
>>>
>>> ERROR 4 [file mCherry7.top, line 25380]:
>>>     No default Proper Dih. types
>>>
>>>
>>> ERROR 5 [file mCherry7.top, line 25383]:
>>>     No default Proper Dih. types
>>>
>>>
>>> ERROR 6 [file mCherry7.top, line 25386]:
>>>     No default Proper Dih. types
>>>
>>>
>>> ERROR 7 [file mCherry7.top, line 25387]:
>>>     No default Proper Dih. types
>>>
>>>
>>> ERROR 8 [file mCherry7.top, line 25388]:
>>>     No default Proper Dih. types
>>>
>>>
>>> ERROR 9 [file mCherry7.top, line 25455]:
>>>     No default Proper Dih. types
>>>
>>>
>>> ERROR 10 [file mCherry7.top, line 25457]:
>>>     No default Proper Dih. types
>>>
>>> ERROR 11 [file mCherry7.top, line 25458]:
>>>     No default Proper Dih. types
>>>
>>>    Now in these files which I have already uploaded I have only added two
>>> extra lines just above [ angles ] section of CH6 residue in aminoacids.rtp
>>> (lines 1793 and 1794):
>>>           MC3     +N      0.1345  154808.0
>>>           MN1     -C      0.139   173594.2
>>>
>>> I have not changed anything else in any other file.
>>> Now the problem is that I have consecutive residues Phe65-CH6-Ser69. MN1
>>> atom of CH6 is supposed to be bonded to C atom of Phe65. MC3 atom of CH6
>>> is
>>> supposed to be bonded to atom NH1 of Ser69. C atom of Phe65 is not
>>> supposed
>>> to be bonded to NH1 atom of Ser69 but it is in my *top file. What other
>>> files do you need?
>>>
>>>
>> The same ones you provided before.
>>
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================